Soft Matter Science - Group Publications


2017

  1. Nana Luo, Jeffrey K. Weber, Shuang Wang, Binquan Luan, Hua Yue, Xiaobo Xi, Jing Du, Zaixing Yang, Wei Wei, R. H. Zhou, Guanghui Ma,
    PEGylated Graphene Oxide Elicits Strong Immunological Responses Despite Surface Passivation,
    Nature Communications, 8, 14537, 2017, DOI:10.1038/ncomms14537
  2. T. Zheng, Z. X. Yang, D. Gui, Z. Liu, X. Wang, X. Dai, S. Liu, L. Zhang, Y. Gao, L. Chen, D. Sheng, Y. Wang, J. Diwu, J. Wang, R. H. Zhou, Z. F. Chai, T. E. Albrecht-Schmitt, and S. Wang,
    Overcoming the crystallization and designability issues in the ultrastable zirconium phosphonate framework system,
    Nature Communications, 8, 15369, 2017, DOI:10.1038/ncomms15369
  3. Zhonghe Xu, Yang Sun, Jeffrey K. Weber, Yi Cao, Wei Wang, Daniel Jasinski, Peixuan Guo, R. H. Zhou, and Jingyuan Li,
    Directional mechanical stability of Bacteriophage ϕ29 motor’s 3WJ-pRNA: extraordinary robustness along portal axis,
    Science Advances, 3, in press, 2017, DOI:10.1126/sciadv.1601684
  4. J. Shen, B. Luan, H. Pei, Z. X. Yang, X. Zuo, G. Liu, J. Shi, L. Wang, R. H. Zhou, W. Cheng, C. H. Fan,
    Hydration-switchable chromogenic films using DNA hybridization-mediated single-nanoparticle-layer plasmonic structures,
    Adv. Mater. 29, in press, 2017
  5. Phil De Luna, Sahar Mahshid, Jagotamoy Das, Binquan Luan, Edward H Sargent, Shana O Kelley, R. H. Zhou,
    High-Curvature Nanostructuring Enhances Probe Display for Biomolecular Detection,
    Nano Lett. 17, 1289–1295, 2017, PMID:28075594
  6. Zonglin Gu, Lin Zhao, Shengtang Liu, Guangxin Duan, Jose M. Perez-Aguilar, Judong Luo, Weifeng Li , and R. H. Zhou,
    Orientational Binding of DNA Guided by the C2N Template,
    ACS Nano, 11, 3198–3206, 2017, DOI: 10.1021/acsnano.7b00236
  7. Xin Tian, Zaixing Yang, Guangxin Duan, Anqing Wu, Zonglin Gu, Leili Zhang, Chunying Chen, Zhifang Chai, Cuicui Ge, and R. H. Zhou,
    Graphene Oxide Nanosheets Retard Cellular Migration via Disruption of Actin Cytoskeleton,
    Small, 13, 1602133, 2017, PMID:27762498
  8. Baoyu Li, Weifeng Li, Jose Manuel Perez-Aguilar, R. H. Zhou,
    Mild Binding of Protein to C2N Monolayer Reveals Its Suitable Biocompatibility,
    Small, 13, 1603685, 2017, PMID:28139876
  9. G. Fang, B. Luan, C. Ge, Y. Chong, X. Dong, J. Guo, C. Tang, R. H. Zhou,
    Understanding the Graphene Quantum Dots-Ubiquitin Interaction by Identifying the Interaction Sites,
    Carbon, 121, in press, 2017
  10. W. Liu, X. Dai, Z. Bai, Y. Wang, Z. X. Yang, L. Zhang, L. Xu, L. Chen, Y. Li, D. Gui, J. Diwu, J. Wang, R. H. Zhou, Z. F. Chai, and S. Wang,
    Highly Sensitive and Selective Uranium Detection in Natural Water Systems Using a Luminescent Mesoporous Metal–Organic Framework Equipped with Abundant Lewis Basic Sites: A Combined Batch, X-ray Absorption Spectroscopy, and First Principles Simulation Investigation,
    Environ. Sci. Technol., 51, 3911–3921, 2017, DOI: 10.1021/acs.est.6b06305
  11. G. Duan, Y. Zhang, B. Luan, J. K. Weber, R. W. Zhou, Z. X. Yang, L. Zhao, J. Xu, J. Luo, and R. H. Zhou,
    Graphene-Induced Pore Formation on Cell Membranes,
    Sci. Rep. 7, 42767, 2017, DOI: 10.1038/srep42767
  12. Mei Feng, David R. Bell, Judong Luo and R. H. Zhou,
    Impact of graphyne on structural and dynamical properties of calmodulin,
    Phys. Chem. Chem. Phys. 19, 10187-10195, 2017, DOI: 10.1039/C7CP00720E
  13. Zonglin Gu, Phil De Luna, Zaixing Yang, R. H. Zhou,
    Structural Influence of Proteins Upon Adsorption to MoS2 Nanomaterials: Comparison of MoS2 Force Field Parameters,
    Phys. Chem. Chem. Phys. 19, 3039-3045, 2017, PMID:28079199
  14. Binquan Luan, R. H. Zhou,
    A Novel Self-Activation Mechanism of Candida antarctica Lipase B,
    Phys. Chem. Chem. Phys. 19, 10.1039/C7CP02198D, in press, 2017
  15. Leili Zhang, Hongsuk Kang, Francisco X. Vázquez, Leticia Toledo-Sherman, Binquan Luan, and R. H. Zhou,
    Molecular Mechanism on Stabilizing Huntingtin N17 Helical Structure in Micelle Environment,
    J. Phys. Chem. B 121, 4713-4721, 2017, DOI:10.1021/acs.jpcb.7b01476
  16. Wei Zhang, Chao Ye, Phil De Luna and R. H. Zhou,
    Snatching the Ligand or Destroying the Structure: Disruption of WW Domain by Phosphorene,
    J. Phys. Chem. C, 121, 1362–1370, 2017, DOI: 10.1021/acs.jpcc.6b10869
  17. Zonglin Gu, Zaixing Yang, Binquan Luan, Xifa Zhou, Linbi Hong, Hong Zhou, Judong Luo, R. H. Zhou,
    Membrane Insertion and Phospholipids Extraction by Graphyne Nanosheets,
    J. Phys. Chem. C, 121, 2444–2450, 2017, DOI: 10.1021/acs.jpcc.6b10548

2016

  1. Binquan Luan, Tien Huynh, Jingyuan Li, R. H. Zhou,
    Nanomechanics of Protein Unfolding Outside a Generic Nanopore,
    ACS Nano 10, 317-323, 2016, PMID: 26655061
  2. Weifeng Li, Yanmei Yang, Jeffrey K. Weber, Gang Zhang, and R. H. Zhou,
    Tunable, Strain-Controlled Nanoporous MoS2 Filter for Water Desalination,
    ACS Nano 10, 1829-1835, 2016, PMID: 26800095
  3. Yuanchao Zhang, Jingquan Liu, Da Li, Xing Dai, Fuhua Yan, R. H. Zhou, Xavier A. Conlan, Colin J. Barrow, Jin He, Xin Wang, Wenrong Yang,
    Self-Assembled Core-Satellite Gold Nanoparticle Networks for Ultrasensitive Detection of Chiral Molecules by Recognition Tunneling,
    ACS Nano, 10, 5096-5103, 2016, PMID: 27104661
  4. Motilal Mathesh, Binquan Luan, Taiwo Akanbia, Jeffrey K. Weber, Jingquan Liu, Colin J. Barrow, R. H. Zhou* and Wenrong Yang*,
    Opening Lids: Modulation of Lipase Immobilization by Graphene Oxides,
    ACS Catalysis, 6, 4760-4768, 2016, DOI: 10.1021/acscatal.6b00942
  5. Binquan Luan, Kai Loon Chen, and R. H. Zhou,
    Mechanism of Divalent-Ion-Induced Charge Inversion of Bacterial Membrane,
    J. Phys. Chem. Lett. 7, 2434-2438, 2016, DOI: 10.1021/acs.jpclett.6b01065
  6. Binquan Luan, Tien Huynh, and R. H. Zhou,
    Complete Wetting of Graphene by Biological Lipids,
    Nanoscale 8, 5750-5754, 2016, PMID: 26910517
  7. Zhonghe Xu, Shuang Zhang, Jeffrey K. Weber, Binquan Luan, R. H. Zhou*, Jingyuan Li,*
    Sequential protein unfolding through a carbon nanotube pore,
    Nanoscale 8, 12143-12151, 2016, PMID: 26899409
  8. Shengtang Liu, Xuan-Yu Meng, Jose Manuel Perez-Aguilar, and R. H. Zhou,
    An In Silico study of TiO2 nanoparticles interaction with twenty standard amino acids in aqueous solution,
    Sci. Rep. 6, 37761, 2016, PMCID:PMC5121885
  9. Wei Zhang, Chao Ye, Linbi Hong, Zaixing Yang, and R. H. Zhou,
    Molecular Structure and Dynamics of Water on Pristine and Strained Phosphorene: Wetting and Diffusion at Nanoscale,
    Sci. Rep. 6, 38327, 2016, PMCID:PMC5138611
  10. Xuan-Yu Meng, Baoyu Li, Shengtang Liu, Hongsuk Kang, Lin Zhao, R. H. Zhou,
    EGCG in Green Tea Induces Aggregation of HMGB1 Protein through Large Conformational Changes with Polarized Charge Redistribution,
    Sci. Rep. 6, 22128, 2016, PMID: 26899177
  11. Yuanzhao Zhang, Jeffrey K. Weber, R. H. Zhou,
    Folding and Stabilization of Native-Sequence-Reversed Proteins,
    Sci. Rep. 6, 25138, 2016, PMID: 27113844
  12. Ramy El-Sayed, Zonglin Gu, Zaixing Yang, Jeffrey K. Weber, Hu Li, Klaus Leifer, Muhammet S. Toprak, R. H. Zhou*, and Bengt Fadeel*,
    Single-Walled Carbon Nanotubes Inhibit the Cytochrome P450 Enzyme, CYP3A4,
    Sci. Rep. 6, 21316, 2016, PMID: 26899743
  13. Zonglin Gu, Zaixing Yang, Seung-gu Kang, Jerry R. Yang, Judong Luo, R. H. Zhou,
    Robust Denaturation of Villin Headpiece by MoS2 Nanosheet: Potential Molecular Origin of the Nanotoxicity,
    Sci. Rep. 6, 28252, 2016, PMID: 27312409
  14. Xuan-Yu Meng, Shengtang Liu, Meng Cui, R. H. Zhou, and Diomedes Logothetis,
    The Molecular Mechanism of Opening the Helix Bundle Crossing (HBC) Gate of a Kir Channel,
    Sci. Rep. 6, 29399, 2016, PMID: 27439597
  15. Binquan Luan,
    Radial dependence of DNA translocation velocity in a solid-state nanopore,
    Microchimia Acta, 183, 995-1002, 2016, DOI: 10.1007/s00604-015-1589-2
  16. Binquan Luan,
    Bio-nano interactions detected by nanochannel electrophoresis,
    Electrophoresis, 7, DOI: 10.1002/elps.201600233, 2016, PMID: 27334561
  17. Zonglin Gu, Yuanzhao Zhang, Binquan Luan, R. H. Zhou,
    DNA translocation through single-layer boron nitride nanopores,
    Soft Matter 12, 817-823, 2016, PMID: 26537824
  18. Binquan Luan, Tien Huynh, and R. H. Zhou,
    Wettability and Friction of Water on a MoS2 nanosheet,
    Appl. Phys. Lett. 108, 131601, 2016, DOI: 10.1063/1.4944840
  19. Binquan Luan, Tien Huynh, and R. H. Zhou,
    Potential Interference of Protein-Protein Interactions by Graphyne,
    J. Phys. Chem. B 120, 2124-2131, 2016, PMID: 26885561
  20. Yang Ling, Zonglin Gu, Seung-gu Kang, Judong Luo, R. H. Zhou,
    Structural damage of a beta-sheet protein upon adsorption onto Molybdenum Disulfide nanotubes,
    J. Phys. Chem. C 120 , 6796-6803, 2016, DOI: 10.1021/acs.jpcc.5b11236
  21. Qingming Deng, Jun Pan, Xiaohui Yin, Xiaofeng Wang, Lina Zhao, Seung-gu Kang, Camilo A. Jimenez-Cruz, R. H. Zhou, Jingyuan Li,
    Toward High Permeability, Selectivity and Controllability of Water Desalination with FePc Nanopores,
    Phys. Chem. Chem. Phys. 18, 8140-8147, 2016, PMID: 26923172
  22. Zonglin Gu, Weifeng Li, Linbi Hong, R. H. Zhou,
    Exploring Biological Effects of MoS2 Nanosheets on Native Structures of α-helical Peptides,
    J. Chem. Phys. 144, 175103, 2016, PMID: 27155655
  23. Mei Feng, Hongsuk Kang, Zaixing Yang, Binquan Luan, R. H. Zhou,
    Potential Disruption of Protein-Protein Interactions by Graphene Oxide,
    J. Chem. Phys. 144, 225102, 2016, PMID: 27306022
  24. Dongling Cao, Jinlin He, Jiaying Xu, Mingzu Zhang, Lin Zhao, Guangxin Duan, Youwen Cao, R. H. Zhou*, and Peihong Ni*,
    Polymeric prodrugs conjugated with reduction-sensitive dextran-camptothecin and pH-responsive dextran-doxorubicin: An effective combinatorial drug delivery platform for cancer therapy,
    Poly. Chem. 7, 4198-4212, 2016,  DOI: 10.1039/C6PY00701E
  25. Yerko Escalona, Jose A. Garate, Raul Araya-Secchi, Tien Huynh, R. H. Zhou, Tomas Perez-Acle,
    Exploring the membrane potential of simple dual-membrane systems as models for Gap-junction channels,
    Biophys. J. 110, 2678-2688, 2016, PMID: 27332126
  26. Lin Zhao, Guangxin Duan, Zaixing Yang, Jeffrey K Weber, Xu Liu, Shunyi Lu, Xuanyu Meng, JiaYing Xu,
    Particle Size-Dependent Antibacterial Activity and Murine Cell Cytotoxicity Induced by Graphene Oxide Nanomaterials,
    Journal of Nanomaterials, 2016, 6709764, 2016, DOI: 10.1155/2016/6709764

2015

  1. Michael C. Baxa, Wookyung Yu, Aashish N. Adhikari, Liang Ge, Zhen Xia, R. H. Zhou, Karl F. Freed, Tobin R. Sosnick,
    Even with non-native interactions, the updated folding transition states of the homologs Protein G & L are extensive and similar,
    Proc. Natl. Acad. Sci., 112, 8302-8307, 2015, PMID: 26100906
  2. Angelique Hölzemer, Christina F. Thobakgale, Camilo A. Jimenez-Cruz, Wilfredo F. Garcia-Beltran, Jonathan M. Carlson, Nienke H. van Teijlingen, Jaclyn K. Mann, Manjeetha Jaggernath, Seung-gu Kang, Christian Körner, Amy W. Chung, Jamie L. Schafer, David T. Evans, Galit Alter, Bruce D. Walker, Philip J. Goulder, Mary Carrington, Pia Hartmann, Thomas Pertel, R. H. Zhou, Thumbi Ndung’u, Marcus Altfeld,
    Selection of an HLA-C*03:04-Restricted HIV-1 p24 Gag Sequence Variant Is Associated with Viral Escape from KIR2DL3+ Natural Killer Cells: Data from an Observational Cohort in South Africa,
    PLoS Medicine, 12, e1001900, 2015, PMID: 26575988
  3. Deyi An, Jiguo Su, Jeffrey K. Weber, Xueyun Gao, R. H. Zhou, Jingyuan Li,
    A peptide-coated gold nanocluster exhibits unique behavior in protein activity inhibition,
    J. Am. Chem. Soc. DOI:10.1021/jacs.5b00888, 2015, PMID: 26084190
  4. B Luan, T Huynh, L Zhao, R Zhou,
    Potential Toxicity of Graphene to Cell Functions via Disrupting Protein-Protein Interactions,
    ACS nano, 2015, PMID: 25494677
  5. Y Chong, C Ge, Z Yang, JA Garate, Z Gu, JK Weber, J Liu, R. H. Zhou,
    Reduced Cytotoxicity of Graphene Nanosheets Mediated by Blood-Protein Coating,
    ACS Nano, 9, DOI: 10.1021/nn5066606, 2015, PMID: 26040772
  6. Yuanming Pan, Liming Wang, Seung-gu Kang, Chengdu Sun, Youyong Lu, Zaixing Yang, Tien Huynh, Chunying Chen, R. H. Zhou, Yuliang Zhao, and Mingzhou Guo,
    Gd-Metallofullerenol Nanomaterial Suppresses Pancreatic Cancer Metastasis by Inhibiting the Interaction of Histone Deacetylase 1 and Metastasis-Associated Protein 1,
    ACS Nano, 9, DOI: 10.1021/nn506782f, 2015, PMID: 26083726
  7. Das, P., Zafar, S. ,
    Mechanistic Influence of Nanometer Length-Scale Surface Chemistry on DNA Hybridization.
    ACS Nano, 2015, 9, 7466, PMID: 26051361
  8. W Li, L Wang, R Zhou, Y Mu,
    Ionic liquid induced inactivation of cellobiohydrolase I from Trichoderma reesei,
    Green Chemistry, 2015, DOI: 10.1039/C4GC02136C
  9. B Luan, T Huynh, R Zhou,
    Nanopore-based Sensors for Ligand-Receptor Lead-Optimization,
    The Journal of Physical Chemistry Letters, 2015, PMID: 26261942
  10. Xiaofeng Wang, Jeffrey K. Weber, Lei Liu, Mingdong Dong, R. H. Zhou, and Jingyuan Li,
    A novel form of β-strand assembly observed in Aβ33–42 adsorbed onto graphene,
    Nanoscale, 7, 15341-15348, 2015, PMID: 26331805
  11. Guangxin Duan, Seung-gu Kang, Xin Tian, Jose Antonio Garate, Lin Zhao, Cuicui Ge, R. H. Zhou,
    Protein corona mitigates the cytotoxicity of graphene oxide by reducing its physical interaction with cell membrane,
    Nanoscale, 7, 15214-15224, 2015, PMID: 26315610
  12. Hua Yue, Wei Wei, Zonglin Gu, Dezhi Ni, Nana Luo, Zaixing Yang, Lin Zhao, Jose Antonio Garate, R. H. Zhou, Zhiguo Su, Guanghui Ma,
    Exploration of graphene oxide as intelligent platform for cancer vaccine,
    Nanoscale, 7, 19949-19957, 2015, PMID: 26419315
  13. Z Yang, C Ge, J Liu, Y Chong, Z Gu, CA Jimenez-Cruz, Z Chai, R. H. Zhou,
    Destruction of amyloid fibrils by graphene through penetration and extraction of peptides,
    Nanoscale 7, 18725-18737, 2015, PMID: 26503908
  14. Wei Zhang, Tien Huynh, Peng Xiu, Bo Zhou, Chao Ye, Binquan Luan, R. H. Zhou,
    Revealing the importance of surface morphology of nanomaterials to biological responses: Adsorption of the villin headpiece onto graphene and phosphorene,
    Carbon, 94, 895-902, 2015, DOI: 10.1016/j.carbon.2015.07.075
  15. Das, P., Murray, B., and Belfort, G.
    Alzheimer’s Protective A2T Mutation Changes the Conformational Landscape of the Aβ 1–42 Monomer Differently Than Does the A2V Mutation.
    Biophysical Journal, 2015, 108, 738, PMID: 25650940
  16. Binquan Luan,
    Numerically testing phenomenological models for conductance of a solid-state nanopore,
    Nanotechnology, 2015, PMID: 25591009
  17. Binquan Luan,
    Radial dependence of DNA translocation velocity in a solid-state nanopore,
    Microchimica Acta, 2015, DOI: 10.1007/s00604-015-1589-2
  18. Binquan Luan, Tien Huynh, R. H. Zhou,
    Simplified TiO2 force fields for studies of its interaction with biomolecules,
    J. Chem. Phys. 142, 234102, 2015, PMID: 26093545
  19. Zonglin Gu, Zaixing Yang, Lingle Wang, Hong Zhou, Camilo A. Jimenez-Cruz, and R. H. Zhou,
    The role of basic residues in the adsorption of blood proteins onto the graphene surface,
    Sci. Rep. 5, 10873, 2015, PMID: 26034971
  20. Zonglin Gu, Zaixing Yang, Yu Chong, Cuicui Ge, Jeffrey K. Weber, David R. Bell and R. H. Zhou,
    Surface Curvature Relation to Protein Adsorption for Carbon-based Nanomaterials,
    Sci. Rep. 5, 10886, 2015, PMID: 26041015
  21. C Ge, J Tian, Y Zhao, C Chen, R Zhou, Z Chai,
    Towards understanding of nanoparticle–protein corona,
    Archives of toxicology, 1-21, 2015, PMID: 25637415
  22. R Song, W Feng, CA Jimenez-Cruz, B Wang, W Jiang, Z Wang, R Zhou,
    Water film inside graphene nanosheets: electron transfer reversal between water and graphene via tight nano-confinement,
    RSC Advances 5 (1), 274-280, 2015, DOI: 10.1039/C4RA13736A
  23. Y Peng, JMJ Swanson, S Kang, R Zhou, GA Voth,
    Hydrated Excess Protons Can Create Their Own Water Wires,
    The Journal of Physical Chemistry B, 2015, PMID: 25369445

2014

  1. G. Stirnemann, S. G. Kang, R. H. Zhou, and B. J. Berne,
    How Force Unfolding Differs from Chemical Denaturation,
    Proc. Natl. Acad. Sci. 111, 3413-3418, 2014, PMID: 24550471
  2. B Song, Q Sun, H Li, B Ge, JS Pan, ATS Wee, Y Zhang, S Huang, R Zhou, ...,
    Irreversible Denaturation of Proteins through Aluminum-Induced Formation of Backbone Ring Structures,
    Angewandte Chemie 126 (25), 6476-6481, 2014, PMID: 24777568
  3. B Luan, B Zhou, T Huynh, R Zhou,
    Controlled transport of DNA through a Y-shaped carbon nanotube in a solid membrane,
    Nanoscale 6 (19), 11479-11483, 2014, PMID: 25154639
  4. C. Guo, Y. Luo, R. H. Zhou, and G. H. Wei,
    Triphenylalanine peptides self-assemble into nanospheres and nanorods that are different from the nanovesicles and nanotubes formed by diphenylalanine peptides,
    Nanoscale, 6, 2800-2811, 2014, PMID: 24468750
  5. J Gao, L Wang, S Kang, L Zhao, M Ji, C Chen, Y Zhao, R Zhou, J Li,
    Size-dependent impact of CNTs on dynamic properties of calmodulin,
    Nanoscale 6 (21), 12828-12837, 2014, PMID: 25225777
  6. W Li, L Nordenskiold, R Zhou, Y Mu,
    Conformation-dependent DNA attraction,
    Nanoscale 6 (12), 7085-7092, 2014, PMID: 24847505
  7. Z. X. Yang, S. G. Kang, and R. H. Zhou,
    Nanomedicine: De Novo Design of Nanodrugs,
    Nanoscale 6, 663-677, 2014, PMID: 24305636
  8. Z. X. Yang, Z. Xia, T. Huynh, J. A. King, and R. H. Zhou,
    Dissecting the contributions of beta-hairpin tyrosine pair to the folding and stability of long-lived human gammaD-crystallins,
    Nanoscale 6, 1797-1807, 2014, PMID: 24352614
  9. CA Jimenez-Cruz, S Kang, R Zhou,
    Large scale molecular simulations of nanotoxicity,
    Wiley Interdisciplinary Reviews: Systems Biology and Medicine 6 (4), 329-343, 2014, PMID: 24894909
  10. R Zhou, H Gao,
    Cytotoxicity of graphene: recent advances and future perspective,
    Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology 6 (5),452-474 ,2014, PMID: 24957946
  11. Y Peng, Z Cao, R Zhou, GA Voth,
    Path Integral Coarse-Graining Replica Exchange Method for Enhanced Sampling,
    Journal of Chemical Theory and Computation 10 (9), 3634-3640, 2014, PMID: 26588508
  12. D.Wang, S. Harrer, B. Luan (co-first), G. Stolovitzky, H. Peng, and A. Afzali-Ardakani,
    Regulating the Transport of DNA through Biofriendly Nanochannels in a Thin Solid Membrane,
    Scientific Report 4, 3985 (2014), PMID: 24496378
  13. J Li, X Wang, L Zhao, X Gao, Y Zhao, R Zhou,
    Rotation Motion of Designed Nano-Turbine,
    Scientific reports 4, PMID: 25068725
  14. S Kang, R Araya-Secchi, D Wang, B Wang, T Huynh, R Zhou,
    Dual inhibitory pathways of metallofullerenol Gd@ C82 (OH) 22 on matrix metalloproteinase-2: Molecular insight into drug-like nanomedicine,
    Scientific reports 4, PMID: 24758941
  15. Y Gao, X Dai, S Kang, CA Jimenez-Cruz, M Xin, Y Meng, J Han, Z Wang, R Zhou,
    Structural and electronic properties of uranium-encapsulated Au14 cage,
    Scientific reports 4, PMID: 25069968
  16. Y Zhang, CA Jimenez-Cruz, J Wang, B Zhou, Z Yang, R Zhou,
    Bio-mimicking of Proline-Rich Motif Applied to Carbon Nanotube Reveals Unexpected Subtleties Underlying Nanoparticle Functionalization,
    Scientific reports 4, 2014, PMID: 25427563
  17. Y. Wang, B. Luan (co-first), Z. Yang, X. Zhang, B. Ritzo, K. Gates and L. Gu,
    Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore,
    Scientific Report 4, 5883 (2014), PMID: 25103463
  18. Z. Xia, H. B. Chen, S. G. Kang, T. Huynh, J. W. Fang, P. A. Lamothe, B. D. Walker, and R. H. Zhou,
    The complex and specific pMHC interactions with diverse HIV-1 TCR clonotypes reveal a structural basis for alterations in CTL function,
    Scientific Report 4, 4087, 2014, PMID: 24522437
  19. R Araya-Secchi, T Perez-Acle, S Kang, T Huynh, A Bernardin, Y Escalona, JA Garate, AD Martínez, IE García IE, JC Sáez, R Zhou,
    Characterization of a novel water pocket inside the human Cx26 hemichannel structure,
    Biophysical journal 107 (3), 599-612, 2014, PMID: 25099799
  20. Fehniger, T. E., Suits, F., Vegvari, A., Horvatovich, P., Foster, M., Marko-Varga G.
    Queries of MALDI-MSI Global Datasets Identifying Ion Mass Signatures Associated With Tissue Compartments
    Proteomics14(7-8):862-71, 2014, PMID: 24478260
  21. M Xin, X Dai, J Han, M Jin, CA Jimenez-Cruz, D Ding, Z Wang, R Zhou,
    Carbon nanotubes adsorb U atoms differently in their inner and outer surfaces,
    RSC Advances 4 (57), 30074-30080, 2014, DOI: 10.1039/C4RA02662D
  22. Y Gao, B Zhou, S Kang, M Xin, P Yang, X Dai, Z Wang, R Zhou,
    Effect of Ligands on Characteristics of (CdSe) 13 Quantum Dot,
    RSC Adv., 2014, DOI: 10.1039/C4RA03202K
  23. B. Luan, C. Wang, A. Royyuru and G. Stolovitzky,
    Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages,
    Nanotechnology 25, 265101 (2014), PMID: 24920303
  24. S Kang, P Das, SJ McGrane, AJ Martin, T Huynh, AK Royyuru, AJ Taylor, ...,
    Molecular Recognition of Metabotropic Glutamate Receptor Type 1 (mGluR1): Synergistic Understanding with Free Energy Perturbation and Linear Response Modeling,
    The Journal of Physical Chemistry B 118 (24), 6393-6404, 2014, PMID: 24635567
  25. Z. W. Cai, J. Q. Li, C. J. Yin, Z. X. Yang, J. L. Wu, and R. H. Zhou,
    Effect of Urea Concentration on Aggregation of Amyloidogenic Hexapeptides (NFGAIL),
    J. Phys. Chem. B 118, 48-57, 2014, PMID: 24328094
  26. J Liu, Z Yang, H Li, Z Gu, JA Garate, R Zhou,
    Dewetting transition assisted clearance of (NFGAILS) amyloid fibrils from cell membranes by graphene,
    The Journal of chemical physics 141 (22), 22D520, 2014, PMID: 25494791
  27. X Dai, Y Gao, M Xin, Z Wang, R Zhou,
    The ground state and electronic structure of Gd@ C82: A systematic theoretical investigation of first principle density functionals,
    The Journal of chemical physics 141 (24), 244306, 2014, PMID: 25554150
  28. X Jiang, J Gao, T Huynh, P Huai, C Fan, R Zhou, B Song,
    An improved DNA force field for ssDNA interactions with gold nanoparticles,
    The Journal of chemical physics 140 (23), 234102, 2014, PMID: 24952518
  29. C. Maffeo, Y. Jejoong, C. Jeffrey, W. David and B. Luan and A. Aksimentiev,
    Close encounters with DNA,
    Journal of Physics: Condensed Matter 26, 413101 (2014), PMID: 25238560
  30. Y. Meng, P. Xiu, B. L. Huang, Z. G. Wang, R. Q. Zhang and R. H. Zhou,
    A unique feature of chiral transition of a difluorobenzo[c]phenanthrene molecule confined in a boron-nitride nanotube based on molecular dynamics simulations,
    Chem. Phys. Lett. 591, 265-267, 2014, doi:10.1016/j.cplett.2013.11.052
  31. O'Donncha, F., Ragnoli, E., Suits, F.
    Parallelisation study of a three-dimensional environmental flow model
    Computers & Geosciences 64(0), 96-103, 2014, doi:10.1016/j.cageo.2013.12.006
  32. R. H. Zhou,
    Biological Water under Confinement: Nanoscale Dewetting,
    MOLECULAR MODELING AT THE ATOMIC SCALE: Methods and Applications in Quantitative Biology (Editor Ruhong Zhou),
    CRC Press, Taylor & Francis, ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014
  33. S. G. Kang and R. H. Zhou,
    Protein and Nanoparticle Interactions: Perspectives of Nanomedicine and Nanotoxicity,
    MOLECULAR MODELING AT THE ATOMIC SCALE: Methods and Applications in Quantitative Biology (Editor Ruhong Zhou),
    CRC Press, Taylor & Francis, ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014
  34. X. H. Huang, R. H. Zhou, and B. J. Berne,
    Introduction to Molecular Dynamics and Enhanced Sampling Algorithms,
    MOLECULAR MODELING AT THE ATOMIC SCALE: Methods and Applications in Quantitative Biology (Editor Ruhong Zhou),
    CRC Press, Taylor & Francis, ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014
  35. Z. Xia and R. H. Zhou,
    Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations,
    MOLECULAR MODELING AT THE ATOMIC SCALE: Methods and Applications in Quantitative Biology (Editor Ruhong Zhou),
    CRC Press, Taylor & Francis, ISBN-10: 1466562951 | ISBN-13: 978-1466562950, 2014

2013

  1. Y. Tu, M. Lv, P. Xiu, T. Huynh, M. Zhang, M. Castelli, Z. R. Liu, Q. Huang, C. H. Fan, H. P. Fang, and R. H. Zhou,
    Destructive Extraction of Phospholipids from E. Coli Membrane by a Graphene Nanosheet,
    Nature Nanotech. 8, 594-601, 2013, doi:10.1038/nnano.2013.125
  2. B. Dai, S. G. Kang, T. Huynh, H. Z. Lei, M. Castelli, J. Hu, Y. Zhang and R. H. Zhou,
    Salts Drive Controllable Multi-Layered Upright Assembly of Amyloid-like Peptides at Mica/Water Interface,
    Proc. Natl. Acad. Sci. 110, 8543-8548, 2013, PMID: 23650355
  3. S. G. Kang, T. Huynh, Z. Xia, Y. Zhang, H. P. Fang, G. H. Wei and R. H. Zhou,
    Hydrophobic Interaction Drives Surface-Assisted Epitaxial Assembly of Amyloid-like Peptides,
    J. Am. Chem. Soc. 135, 3150-3157, 2013, PMID: 23360070
  4. P. Das, D. Kapoor, K. T. Halloran, R. H. Zhou, and C. R. Matthews,
    Interplay between Drying and Stability of a TIM Barrel Protein: A Combined Simulation-Experimental Study,
    J. Am. Chem. Soc. 135, 1882-1890, 2013, PMID: 23293932
  5. G. H. Zuo, S. G. Kang, P. Xiu, Y. L. Zhao, and R. H. Zhou,
    Interactions between Proteins and Carbon-Based Nanoparticles: Exploring the Origin of Nanotoxicity at Molecular Level,
    Small 9, 1546-1556, 2013, PMID: 23038664
  6. X. Yin, L. Zhao, S. G. Kang, J. Pan, Y. Song, M. Zhang, G. Xing, F. Wang, J. Y. Li, R. H. Zhou, Y. L. Zhao,
    Impacts of Fullerene Derivatives to Regulate the Structure and Assembly of Collagen Molecules,
    Nanoscale 5, 7341-7348, 2013, PMID: 23820497
  7. S. G. Kang, T. Huynh, and R. H. Zhou,
    Metallofullerenol Gd@C82(OH)22 Distracts Proline-Rich-Motif from Putative Binding on SH3 domain,
    Nanoscale 5, 2703-2712, 2013, PMID: 23423582
  8. Z. Xia, Z. X. Yang, T. Huynh, J. A. King, and R. H. Zhou,
    UV-radiation Induced Disruption of Tightly Packed Dry Cavities in Human gamma D-crystallin Results in Decreased Stability and Faster Unfolding,
    Sci. Rep. 3, 1560, 2013, PMID: 23532089
  9. Y. Tu , H. Lu, Y. Z. Zhang, T. Huynh, and R. H. Zhou,
    Capability of Charge Signal Conversion and Transmission by Water Chains Confined inside Y-Shaped Carbon Nanotubes,
    J. Chem. Phys. 138, 015104, 2013, PMID: 23298064
  10. X. Y. Zhou, C. L. Wang, F. Wu, M. Feng, J. Y. Li, H. J. Lu, R. H. Zhou,
    The Ice-like Water Monolayer near the Wall Makes Inner Water Shells Diffuse Faster inside a Charged Nanotube,
    J. Chem. Phys. 138, 204710, 2013, PMID: 23742503
  11. B. Y. Shi, G. H. Zuo, P. Xiu, and R. H. Zhou,
    Binding Preference of Carbon Nanotube Over Proline-Rich Motif Ligand on SH3-domain: A Comparison with Different Force Fields,
    J. Phys. Chem. B 117, 3541-3547, 2013, PMID: 23477344
  12. Suits, F., Fehniger, T. E., Vegari, A., Marko-Varga, G., Horvatovich, P.
    Correlation Queries for Mass Spectrometry Imaging
    Analytical Chemistry 85(9), 4398-4404, 2013, PMID: 23537055
  13. P. Das, Z. Xia, R. H. Zhou,
    Collapse of A Hydrophobic Polymer in Mixture of Denaturants,
    Langmuir 29, 4877-4882, 2013, PMID: 23517381
  14. C. Christin, H.C.J. Hoefsloot, A.K. Smilde, B. Hoekman, F. Suits, R. Bischoff, P. Horvatovich
    A critical assessment of feature selection methods for biomarker discovery in clinical proteomics,
    Molecular & Cellular Proteomics 12(1), 263-276, ASBMB, 2013, PMID: 23115301
  15. Z. Xia, T. Huynh, P. Y. Ren and R. H. Zhou,
    Large Domain Motions in Ago Protein Controlled by the Guide Strand Seed Region Determine the Ago Silencing Complex Recognition Process,
    PLoS ONE 8, e54620, 2013, PMID: 23382927
  16. X. P. Ren, C. L. Wang, B. Zhou, H. P. Fang, J. Hu, and R. H. Zhou,
    Ethanol Promotes Dewetting Transition at Low Concentrations,
    Soft Matter, 9, 4655-4660, 2013, DOI: 10.1039/C3SM00049D
  17. Horvatovich, P., Suits, F., Hoekman, B., Bischoff, R.
    CHAPTER 7 Bioinformatics and Statistics: LC-MS(/MS) Data Preprocessing for Biomarker Discovery
    Comprehensive Biomarker Discovery and Validation for Clinical Application, pp. 199-225, The Royal Society of Chemistry, 2013, DOI:10.1039/9781849734363-00199
  18. P Xiu, R Zhou, Z Xia,
    Small Molecules and Peptides Inside Carbon Nanotubes: Impact of Nanoscale Confinement,
    INTECH Open Access Publisher, PDF
  19. B. Luan, J. Bai and G. Stolovitzky,
    Fabricatable nanopore sensors with an atomic thickness,
    Appl. Phys. Lett. , 103, 183501 (2013), DOI: 10.1063/1.4826599
  20. B. Luan and G. Stolovitzky,
    An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation,
    Nanotechnology , 24, 195702 (2013), PMID: 23579206
  21. B. Luan,
    Modelling of DNA sequencing with solid-state nanopores,
    Molecular Modeling at the Atomic Scale - Methods and Applications in Quantitative Biology Edited by Ruhong Zhou, (2013)

2012

  1. P. Ntziachristos, A. Tsirigos, P. Van Vlierberghe, J. Nedjic, T. Trimarchi, M. Sol Flaherty, D. Ferres-Marco, V. da Ros, Z. Tang, J. Siegle, P. Asp, M. Hadler, I. Rigo, K. D. Keersmaecker, J. Patel, T. Huynh, F. Utro, S. Poglio, J. B. Samon, E. Paietta, J. Racevskis, J. M. Rowe, R. Rabadan, R. L. Levine, S. Brown, F. Pflumio, M. Dominguez, A. Ferrando, and I. Aifantis,
    Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia,
    Nature Medicine, 18, 298-303, 2012, PMID: 22237151
  2. S. G. Kang, G. Q. Zhou, P. Yang, Y. Liu, B. Y. Sun, T. Huynh, H. Meng, L. Zhao, G. M. Xing, C. Y. Chen, Y. L. Zhao, R. H. Zhou,
    Molecular Mechanism of Pancreatic Tumor Metastases Inhibition by Metallofullerenol Gd@C82(OH)22: Implication for de novo Design of Nanomedicine,
    Proc. Natl. Acad. Sci., 109, 15431-15436, 2012 (featured article), PMID: 22949663
  3. L. Cong, R. H. Zhou, Y. C. Kuo, M. Cunniff, and F. Zhang,
    Comprehensive Interrogation of Natural TALE DNA Binding Modules and Transcriptional Repressor Domains,
    Nature Commun. 3, 968, 2012, PMID: 22828628
  4. Z. Xia, P. Das, E. I. Shakhnovich, and R. H. Zhou,
    Collapse of Unfolded Proteins in a Mixture of Denaturants,
    J. Am. Chem. Soc. 134, 18266-18274, 2012, PMID: 23057830
  5. S.G. Kang, H. Li, T. Huynh, F. Zhang, Z. Xia, Y. Zhang and R. H. Zhou,
    Molecular Mechanism of Surface-Assisted Epitaxial Self-Assembly of Amyloid-like Peptides,
    ACS Nano, 6, 9276-9282, 2012, PMID: 23002915
  6. C. Guo, Y. Luo, R. H. Zhou, and G. H. Wei,
    Dissecting the self-assembly pathway of diphenylalanine-based nanovesicles and nanotubes,
    ACS Nano, 6, 3907-3918, 2012, PMID: 22468743
  7. P Das
    Effect of cosolvents on nano-confined water: a molecular dynamics study
    Nanoscale, 4, 2031-2936, 2012, PMID: 22441726
  8. B. Luan, G Stolovitzky, G Martyna
    Slowing and controlling the translocation of DNA in a solid-state nanopore
    Nanoscale 4(4), 1068-1077, The Royal Society of Chemistry, 2012, PMID: 22081018
  9. Amanda Barnard, Changming Li, R. H. Zhou, Y. L. Zhao,
    Modeling of nanoscale,
    Nanoscale, 4, 1042-1043, 2012, DOI: 10.1039/C2NR90005J
  10. P. Xiu, Y. Tu, X. L. Tian, H. P. Fang, and R. H. Zhou,
    Molecular Wire of Urea in Carbon Nanotube: A Molecular Dynamics Study,
    Nanoscale, 4, 652-658, 2012, PMID: 22159294
  11. S. G. Kang, T. Huynh, and R. H. Zhou,
    Metallofullerenol Gd@C82(OH)22 Non-destructively Inhibits Signal Transduction Pathway of WW domain,
    Sci. Rep. 2, 957, 2012, doi:  10.1038/srep00957
  12. Z. Xia, P. Clark, T. Huynh, P. Loher, Y. Zhao, H.W. Chen, P. Y. Ren, I. Rigoutsos, and R. H. Zhou,
    Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets,
    Sci. Rep. 2, 569, 2012, PMID: 22888400
  13. Z. X. Yang, Z. Wang, X. L. Tian, P. Xiu, and R. H. Zhou,
    Amino Acid Analogues Bind to Carbon Nanotube via pi-pi interactions: Comparison of Molecular Mechanical and Quantum Mechanical Calculations,
    J. Chem. Phys. 136, 025103, 2012, PMID: 22260616
  14. X. Y. Li, Y. C. Shi, Y. L. Yang, H. L. Du, R. H. Zhou, and Y. L. Zhao,
    How does water-nanotube interaction influence water flow through the nanochannel?
    J. Chem. Phys. 136, 175101, 2012, PMID: 22583266
  15. T. Y. Yoo, A. Adhikari, Z. Xia, T. Huynh, K. F. Freed, R. H. Zhou, T. R. Sosnick,
    The folding transition state of protein L is extensive with non-native interactions,
    J. Mol. Biol. 420, 220-234, 2012, PMID: 22522126
  16. W. F. Li, R. H. Zhou, and Y. G. Mu,
    Salting effects on protein components in aqueous NaCl and urea solutions: toward understanding of urea-induced protein denaturation,
    J. Phys. Chem. B 116, 1446-1451, 2012, PMID: 22216970
  17. Z. X. Yang, P. Xiu, B. Y. Shi, L. Hua, and R. H. Zhou,
    A coherent microscopic picture for urea-induced denaturation of proteins,
    J. Phys. Chem. B 116, 8856-8862, 2012, PMID: 22780326
  18. P Das, S Matysiak
    Direct Characterization of Hydrophobic Hydration during Cold and Pressure Denaturation
    J. Phys. Chem. B, ACS publications, 2012, PMID: 22512347
  19. L. Zhao, Y. L. Zhao, and R. H. Zhou,
    Novel design of a nanoflowmeter based on carbon nanotubes,
    J. Phys. Chem. C, 116, 13429-13434, 2012, DOI: 10.1021/jp302895a
  20. B. Q. Luan and R. H. Zhou,
    Nanopore Sensor for Detecting Nanotoxicity of a Carbon Nanotube to Proteins,
    J. Phys. Chem. Lett. 3, 2337-2341, 2012, PMID: 23002420
  21. T. Rosenling, M.P. Stoop, A. Attali, H. Aken, E. Suidgeest, C. Christin, C. Stingl, F. Suits, P. Horvatovich, R.Q. Hintzen, others
    Profiling and identification of cerebrospinal fluid proteins in a rat EAE model of multiple sclerosis
    Journal of Proteome Research 11(4), 2048--2060, ACS Publications, 2012, PMID: 22320401
  22. Z. Xia, T. Huynh, S. G. Kang, and R. H. Zhou,
    Free Energy Simulations Reveal Both Hydrophobic and Polar Interactions are Important to Influenza Hemagglutinin Antibody Binding,
    Biophys. J. 102, 1453-1461, 2012, PMID: 22455929
  23. S. C. Flores, J. Bernauer, S. Shin, R. H. Zhou, and X. Huang,
    Multiscale modeling of macromolecular biosystems,
    Briefings in Bioinformatics, 13, 395-405, 2012, PMID: 22228511
  24. C. J. Tian, P. Xiu, Y. Meng, W. Y. Zhao, Z. G. Wang, and R. H. Zhou,
    Mechanism of Chiral Inversion of Thalidomide and the Role of Water and Hydroxide Ion,
    Chem. Eur. J. 18, 14305-14313, 2012 (cover article), DOI: 10.1002/chem.201202651
  25. G. Zuo, P. Xiu, X. Zhou, R. H. Zhou, and H. P. Fang,
    Conformational Changes of the Protein Domains Upon Binding with Carbon Nanotubes Studied by Molecular Dynamics Simulations
    Curr. Phys. Chem., 2, 12-22, 2012, DOI: 10.2174/1877946811202010012
  26. R. H. Zhou,
    Protein folding: Bridging the gap between theory and experiment,
    Curr. Phys. Chem., 2, 2-3, 2012 (Editorial for Hot-topic Special Issue), DOI: 10.2174/1877946811202010002
  27. B. Hoekman, R. Breitling, F. Suits, R. Bischoff, P. Horvatovich
    msCompare: A Framework for Quantitative Analysis of Label-free LC-MS Data for Comparative Candidate Biomarker Studies
    Molecular & Cellular Proteomics 11(6), ASBMB, 2012,  PMID: 22318370
  28. B. Q. Luan, D. Q. Wang, R. H. Zhou, S. Harrer, H. B. Peng, and G. Stolovitzky,
    Dynamics of DNA Translocation in a Solid-State Nanopore Immersed in Aqueous Glycerol,
    Nanotechnology, 23, 455102, 2012, PMID: 23064727
  29. Christopher Maffeo, Binquan Luan, Aleksei Aksimentiev
    End-to-end attraction of duplex DNA
    Nucleic acids research 40(9), 3812--3821, Oxford Univ Press, 2012, PMID: 22241779
  30. Z. Xia, P. Xiu, and R. H. Zhou,
    Small Molecules and Peptides inside Carbon Nanotubes: Impact of Nanoscale Confinement,
    Recent Progress in Carbon Nanotube Research (Editor A. Lazinica), ISBN 980-953-307-485-1, InTech Publisher, 2012, PDF
  31. Ragnoli, E.; Zhuk, S. ; Donncha, F.O. ; Suits, F. ; Hartnett, M.
    An optimal interpolation scheme for assimilation of HF radar current data into a numerical ocean model
    Oceans, 2012, pp. 1-5, IEEE, DOI: 10.1109/OCEANS.2012.6404901
  32. Donncha, F.O. and Ragnoli, E. and Zhuk, S. and Suits, F.
    Surface flow dynamics within an exposed wind-driven bay: Combined HF radar observations and model simulations
    Oceans, 2012, pp. 1-8, DOI: 10.1109/OCEANS.2012.6404902

2011

  1. C. Ge, J. F. Du, L. Zhao, L. Wang, Y. Liu, D. H. Li, Y. Yang, R. H. Zhou, Y. L. Zhao, Z. F. Chai, C. Y. Chen,
    Binding of human serum proteins on single-wall carbon nanotubes reduces cytotoxicity,
    Proc. Natl. Acad. Sci. 108, 16968-16973, 2011 (featured article), PMID: 21969544
  2. P. Das, J. A. King, and R. H. Zhou,
    Aggregation of gamma-Crystallins Associated with Human Cataracts via Domain Swapping at the C-terminal beta-strands,
    Proc. Natl. Acad. Sci., 108, 10514-10519, 2011 (featured article), PMID: 21670251
  3. Z. X. Yang, B. Y. Shi, H. J. Lu, P. Xiu, and R. H. Zhou,
    Dewetting transitions in the self-assembly of two amyloidogenic β-sheets and the importance of matching surfaces,
    J. Phys. Chem. B 115, 11137-11144, 2011, PMID: 21863898
  4. P. Xiu, Z. Yang, B. Zhou, P. Das, H. P. Fang and R. H. Zhou,
    Urea-Induced Drying of Hydrophobic Nanotubes: Comparison of Different Urea Models,
    J. Phys. Chem. B, 115, 2988-2994, 2011, PMID: 21384841
  5. R. H. Zhou, J. Li, L. Hua, Z. Yang, and B. J. Berne,
    Comment on "Urea-Mediated Protein Denaturation: A Consensus View",
    J. Phys. Chem. B, 115, 1323-1326, 2011, PMID: 21247088
  6. G. Zuo, X Zhou, Q Huang, H. P. Fang, and R. H. Zhou,
    Adsorption of Villin Headpiece onto Graphene, Carbon Nanotube and C60: Effect of Contacting Surface Curvatures on Binding Affinity,
    J. Phys. Chem. C 115, 23323-23328, 2011, DOI: 10.1021/jp208967t
  7. G. Zuo, W. Gu, H. P. Fang, and R. H. Zhou,
    Carbon Nanotube Wins the Competitive Binding over Proline-Rich Motif Ligand on SH3 Domain
    J. Phys. Chem. C, 12322-12328, 2011, DOI: 10.1021/jp2026303
  8. F. Suits, B. Hoekman, T. Rosenling, R. Bischoff, P. Horvatovich
    Threshold-Avoiding Proteomics Pipeline
    Analytical chemistry 83(20), 7786--7794, ACS Publications, 2011, PMID: 21879761
  9. I. Ahmad, F. Suits, B. Hoekman, M.A. Swertz, H. Byelas, M. Dijkstra, R. Hooft, D. Katsubo, B. van Breukelen, R. Bischoff, others
    A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data
    Bioinformatics 27(8), 1176--1178, Oxford Univ Press, 2011, PMID: 21349866
  10. M. Reumann, B.G. Fitch, A. Rayshubskiy, M.C. Pitman, J.J. Rice
    Orthogonal recursive bisection as data decomposition strategy for massively parallel cardiac simulations
    Biomedizinische Technik/Biomedical Engineering 56(3), 129--145, Walter de Gruyter, 2011, PMID: 21657987
  11. B. Luan, G. Stolovitzky, H. Peng, S. Harrer, P. Waggoner, S. Polonsky, S. Rossnagel, and G. Martyna
    Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore
    Biophysical Journal 100(3), 168, Elsevier, 2011, PMID: 22067161
  12. T. Rosenling, M.P. Stoop, A. Smolinska, B. Muilwijk, L. Coulier, S. Shi, A. Dane, C. Christin, F. Suits, P.L. Horvatovich, others
    The impact of delayed storage on the measured proteome and metabolome of human cerebrospinal fluid
    Clinical chemistry 57(12), 1703--1711, Am Assoc Clin Chem, 2011, PMID: 21998343
  13. S. Harrer, P. S. Waggoner, B. Luan, A. Afzali-Ardakani, D. L. Goldfarb, H. Peng, G. Martyna, S. M. Rossnagel, G. A. Stolovitzky
    Electrochemical Protection of Thin Film Electrodes in Solid State Nanopores
    Nanotechnology 22(27), 275304, IOP Publishing, 2011, PMID: 21597142
  14. Z. Xia, P. Das, T. Huynh, A. K. Royyuru, and R. H. Zhou,
    Modeling Mutations of Influenza Virus with IBM Blue Gene,
    IBM J. Res. Dev., 55, 7:1-7:11, 2011, PDF
  15. G. Zuo, H. P. Fang, and R. H. Zhou,
    Nanotoxicity: Exploring the interactions between carbon nanotubes and proteins,
    Carbon Nanotubes -Growth and Applications (Editor J. M. Marulanda), pp539-564, InTech Publisher, ISBN 978-953-307-566-2, 2011, DOI: 10.5772/17245
  16. H Peng, B Luan, G Stolovitzky
    Nanopore-Based DNA Sequencing and DNA Motion Control
    Nanopores: Sensing and Fundamental Biological Interactions; Iqbal, Samir M. and Bashir, Rashid (Eds.) , pp. 255, Springer Verlag, 2011, DOI: 10.1007/978-1-4419-8252-0_11
  17. J Li ; B Luan ; Hsu, T.H. ; Zhu, Y. ; Martyna, G. ; Newns, D. ; Cheng, H.Y. ; Raoux, S. ; Lung, H. L. ; Lam, C.
    Explore physical origins of resistance drift in phase change memory and its implication for drift-insensitive materials
    Electron Devices Meeting (IEDM), 2011 IEEE International , pp. 12.5.1 - 12.5.4, DOI: 10.1109/IEDM.2011.6131541
  18. J. Bernauer, S. C. Flores, X. Huang, S. Shin, R. H. Zhou,
    Introduction to Multi-Scale Modelling of Biosystems: From Molecular to Mesoscale,
    Pacific Symposium on Biocomputing 16:177-180, 2011, PDF
  19. B.J. Pope, B.G. Fitch, M.C. Pitman, J.J. Rice, M. Reumann
    Petascale computation performance of lightweight multiscale cardiac models using hybrid programming models
    Engineering in Medicine and Biology Society, EMBC, 2011 Annual International Conference of the IEEE, pp. 433--436, PMID: 22254341

2010

  1. L. Laurent, E. Wong, G. L. Li, T. Huynh, A. Tsirigos, C. T. Ong, H. M. Low, K. W. K. Sung, I. Rigoutsos, J. Loring, C. L. Wei,
    Dynamic changes in the human methylome during differentiation
    Genome Research 20 (3), 320-331, 2010, PMID: 20133333
  2. B Luan, H Peng, S Polonsky, S Rossnagel, G Stolovitzky, G Martyna
    Base-By-Base Ratcheting of Single Stranded DNA through a Solid-State Nanopore
    Physical Review Letters 104(23), 238103, APS, 2010, PMID: 20867275
  3. G. Zuo, Q. Huang, G. Wei, R. H. Zhou, and H. Fang,
    Plugging Into Proteins: Poisoning Protein Function by a Hydrophobic Nanoparticle,
    ACS Nano, 4, 7508-7514, 2010, PMID: 21080666
  4. Y. Tu, R. H. Zhou, and H. Fang,
    Signal transmission, conversion and multiplication by polar molecules confined in nanochannels,
    Nanoscale, 2, 1976-1983, 2010 (featured article), PMID: 20820644
  5. D P Hurst, A Grossfield, D L Lynch, S Feller, T D Romo, K Gawrisch, M C Pitman, P H Reggio
    A lipid pathway for ligand binding is necessary for a cannabinoid G protein-coupled receptor
    Journal of Biological Chemistry 285(23), 17954, ASBMB, 2010, PMID: 20220143
  6. J. A. Morrone, R. H. Zhou, and B. J. Berne,
    Molecular dynamics with multiple time scales: How to avoid pitfalls,
    J. Comp. Theo. Chem., 6, 1798-1804, 2010, PMID: 26615840
  7. Binquan Luan, Ali Afzali, Stefan Harrer, Hongbo Peng, Philip Waggoner, Stas Polonsky, Gustavo Stolovitzky, Glenn Martyna
    Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer
    J. Phys. Chem. B 114(51), 17172-17176, 2010, PMID: 21128651
  8. M. Gao, Z. She, and R. H. Zhou,
    Key residues that play a critical role in lysozyme denaturing in 8M urea,
    J. Phys. Chem. B 114, 15687-15693, 2010, PMID: 21053934
  9. J. Li, P. Das, R. H. Zhou,
    Single mutation effects on conformational change and membrane deformation of influenza Hemagglutinin fusion peptides,
    J. Phys. Chem. B, 114, 8799-8806, 2010, PMID: 20552971
  10. P. Das, R. H. Zhou,
    Urea-induced drying of carbon nanotubes suggests existence of a dry globule-like transient state during chemical denaturation of proteins
    J. Phys. Chem. B, 114, 5427-5430, 2010, PMID: 20361766
  11. B Luan, A Aksimentiev
    Control and Reversal of the Electrophoretic Force on DNA in a Charged Nanopore
    Journal of Physics: Condensed Matter 22, 454123, IOP Publishing, 2010, PMID: 21339610
  12. C Christin, H C Hoefsloot, A K Smilde, F Suits, R Bischoff, P L Horvatovich
    Time alignment algorithms based on selected mass traces for complex LC-MS data
    J Proteome Res 9(3), 1483-95, 2010, PMID: 20070124
  13. T D Romo, A Grossfield, M C Pitman
    Concerted Interconversion between Ionic Lock Substates of the $\beta$2 Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics
    Biophysical journal 98(1), 76, The Biophysical Society, 2010, PMID: 20074514
  14. Z. Wang, C. Wang, P. Xiu, W. Qi, Y. Tu, Y. Shen, R. H. Zhou, R. Zhang, and H. Fang,
    Size Dependence of Nanoscale Confinement on Chiral Transformation,
    Chem. Eur. J., 16, 6482-6487, 2010, PMID: 20486102
  15. S. Harrer, S. Ahmed, A. Afzali-Ardakani, B. Luan, P. S. Waggoner, X. Shao, H. Peng, D. L. Goldfarb, G. J Martyna, S. M. Rossnagel, L. Deligianni, G. A. Stolovitzky
    Electrochemical Characterization of Thin Film Electrodes Toward Developing a DNA Transistor
    Langmuir 26(24), 153103--153103, ACS Publications, 2010, PMID: 21090688
  16. S Cheng, B Luan, M. Robbins
    Contact and friction of nano-asperities: effects of absorbed monolayers
    Physics Review E, 2010, PMID: 20365427
  17. B Luan, R Carr, M Caffrey, A Aksimentiev
    The effect of calcium on the conformation of cobalamin transporter BtuB
    Proteins: Structure, Function, and Bioinformatics 78(5), 1153--1162, Wiley Online Library, 2010, PMID: 19927326
  18. P. Das, J. A. King, and R. H. Zhou,
    beta-strand interactions at the domain interface critical for the stability of human lens gammaD-crystallin,
    Prot. Sci., 19, 131-140, 2010, PMID: 19937657
  19. Binquan Luan, Aleksei Aksimentiev
    Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes
    Soft Matter 6(2), 243--246, Royal Society of Chemistry, 2010, PMID: 20563230
  20. J. Bernauer, S. C. Flores, X. Huang, S. Shin and R. H. Zhou,
    Multi-resolution modeling of biological macromolecules, PDF
    Pacific Symposium on Biocomputing, 15, 200-204, 2010
  21. Tien Huynh, Michail Vlachos, Isidore Rigoutsos
    Anchoring millions of distinct reads on the human genome within seconds
    Proceedings of the 13th International Conference on Extending Database Technology, pp. 252--262, 2010, PDF

2009

  1. Y. Tu, P. Xiu, R. Wan, J. Hu, R. H. Zhou and H. Fang,
    Water-mediated signal multiplication with Y-shaped carbon nanotubes,
    Proc. Natl. Acad. Sci., 106, 18120-18124, 2009, PMID: 19815515
  2. R. Zangi, R. H. Zhou, and B. J. Berne,
    Urea's Action on Hydrophobic Interactions,
    J. Am. Chem. Soc., 131, 1535-1541, 2009, PMID: 19123816
  3. B. J. Berne, J. D.Weeks, and R. H. Zhou,
    Dewetting and Hydrophobic Interaction in Physical and Biological Systems,
    Annu. Rev. Phys. Chem., 60, 85?103, 2009, PMID: 18928403
  4. P. Das, J. Li, A. K. Royyuru, and R. H. Zhou,
    Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity
    J. Comp. Chem. Special Issue on Free Energy Perturbation, Vol. 30, 1654-1633, 2009, PMID: 19399777
  5. Z. Xia, J. Gu, J. Zhu and R. H. Zhou,
    Using a Mutual Information Based Site Transition Network to Map the Genetic Evolution of Influenza A/H3N2 Virus,
    Bioinformatics, 25, 2309-2317, 2009, PMID: 19706746
  6. Z. Xia, Z. Zhu, J. Zhu, and R. H. Zhou,
    Recognition Mechanism of siRNA by Viral p19 Suppressor of RNA Silencing: A Molecular Dynamics Study,
    Biophys. J., 96, 1761-1769, 2009, PMID: 19254536
  7. D Lynch, D Hurst, P Reggio, A Grossfield, M Pitman
    Atomic Level Description of GPCR Activation Revealed by Microsecond Time Scale Molecular Dynamics
    Biophysical Journal 96(3S1), 365--365, Elsevier, 2009, DOI: http://dx.doi.org/10.1016/j.bpj.2008.12.1965
  8. Antonios Tavlarakis and R. H. Zhou,
    Linear interaction energy approximation for binding affinities of nevirapine and HEPT analogues with HIV-1 reverse transcriptase,
    Mol. Simul., 35, 1224-1241, 2009, DOI: 10.1080/08927020902929828
  9. G Khelashvili, A Grossfield, S E Feller, M C Pitman, H Weinstein
    Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations
    Proteins: Structure, Function, and Bioinformatics 76(2), 403--417, Wiley Online Library, 2009, PMID: 19173312
  10. Binquan Luan, Mark O Robbins
    Hybrid atomistic/continuum study of contact and friction between rough solids
    Tribology Letters 36(1), 1--16, Springer, 2009, DOI: 10.1007/s11249-009-9453-3
  11. M Reumann, BG Fitch, A Rayshubskiy, DU Keller, G Seemann, O Doessel, MC Pitman, JJ Rice
    Orthogonal recursive bisection data decomposition for high performance computing in cardiac model simulations: Dependence on anatomical geometry.
    Conf proc IEEE Eng Med Biol Soc, pp. 2799, 2009, PMID: 19964263
  12. M Reumann, BG Fitch, A Rayshubskiy, D Keller, G Seemann, O Dossel, MC Pitman, JJ Rice
    Strong scaling and speedup to 16,384 processors in cardiac electro?Mechanical simulations
    Engineering in Medicine and Biology Society, 2009, pp. 2795--2798, PMID: 19964262
  13. Blake G Fitch, Aleksandr Rayshubskiy, Michael C Pitman, Christopher T J Ward, Robert S Germain
    Using the Active Storage Fabrics model to address petascale storage challenges
    Proceedings of the 4th Annual Workshop on Petascale Data Storage, pp. 47--54, ACM, 2009, DOI: 10.1145/1713072.1713086

2008

  1. L. Hua, R. H. Zhou, D. Thirumalai, B. J. Berne,
    Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding,
    Proc. Natl. Acad. Sci., 105, 16928-16933, 2008, PMID: 18957546
  2. M. G. Krone, L. Hua, P. Soto, R. H. Zhou, B. J. Berne, and J-E. Shea,
    Role of Water in Mediating the Assembly of Alzheimer Amyloid-beta Abeta16-22 Protofilaments,
    J. Am. Chem. Soc., 130, 11066-11072, 2008, PMID: 18661994
  3. A Grossfield, M C Pitman, S E Feller, O Soubias, K Gawrisch
    Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin
    Journal of molecular biology 381(2), 478--486, Elsevier, 2008, PMID: 18585736
  4. R. H. Zhou, P. Das, A. K. Royyuru,
    Single Mutation Induced H3N2 Hemagglutinin Antibody Neutralization: A Free Energy Perturbation Study, Cover article,
    J. Phys. Chem. B, 112, 15813-15820, 2008, PMID: 19367871
  5. R. H. Zhou, M. Eleftheriou, C.-C. Hon, R. S. Germain, A. K. Royyuru, and B. J. Berne,
    Massively parallel molecular dynamics simulations of lysozyme unfolding,
    IBM J. Res. Dev., 52, 19-30, 2008, PDF
  6. L. Ye, T. Liu, Z. Wu, and R. H. Zhou,
    Sequence-based protein domain boundary prediction using BP neural network with various property profiles,
    Proteins, 71, 300-307, 2008, PMID: 19367871
  7. G Khelashvili, A Grossfield, S E Feller, M C Pitman, H Weinstein
    Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations
    Proteins: Structure, Function, and Bioinformatics 76(2), 403--417, John Wiley \& Sons, 2008, PMID: 19173312
  8. B G Fitch, A Rayshubskiy, M Eleftheriou, TJ Ward, M Giampapa, M C Pitman, J Pitera, W C Swope, R S Germain
    Blue matter: scaling of N-body simulations to one atom per node
    Current Topics in Membranes 60, 159--180, Elsevier, 2008, DOI: 10.1016/S1063-5823(08)00006-9
  9. M Reumann, BG Fitch, A Rayshubskiy, DL Weiss, G Seemann, O Doessel, MC Pitman, JJ Rice
    Error estimates and communication overhead in the computation of the bidomain equations on the distributed memory parallel Blue Gene/L supercomputer
    Computers in Cardiology, 2008, 81--84, DOI: 10.1109/CIC.2008.4748982
  10. M Reumann, B G Fitch, A Rayshubskiy, D U Keller, D L Weiss, G Seemann, O Doessel, M C Pitman, J J Rice
    Large scale cardiac modeling on the Blue Gene supercomputer
    Conf proc IEEE Eng Med Biol Soc, pp. 577--580, 2008, PMID: 19162721

2007

  1. R. H. Zhou, M. Eleftheriou, A. Royyuru, B. J. Berne,
    Destruction of long-range interactions by a single mutation in lysozyme,
    Proc. Natl. Acad. Sci., 104, 5824-5829, 2007, PMID: 17389393
  2. J. Li, X. Gong, H. Lu, D. Li, H. Fang and R. H. Zhou,
    Electrostatic Gating of a Nanometer Water Channel,
    Proc. Natl. Acad. Sci., 104, 3687-3692, 2007, PMID: 17360413
  3. P W Lau, A Grossfield, S E Feller, M C Pitman, M F Brown
    Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations
    Journal of molecular biology 372(4), 906--917, Elsevier, 2007, PMID: 17719606
  4. L. Hua, X. Huang, P. Liu, R. H. Zhou, and B. J. Berne,
    Nanoscale Dewetting Transition in Protein Complex Folding,
    J. Phys. Chem. B, 111, 9069-9077, 2007, PMID: 17608515
  5. X. Huang, M. Hagen, B. Kim, R. A. Friesner, R. H. Zhou, and B. J. Berne,
    Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems,
    J. Phys. Chem. B, 111, 5405-5410, 2007, PMID: 17439169
  6. L. Ye, Z. Wu, M. Eleftheriou, and R. H. Zhou,
    Single-mutation-induced stability loss in protein lysozyme,
    Biochem. Soc. Trans., 35, 1551-1557, 2007, PMID: 18031265
  7. R. H. Zhou, L. Parida, K. Kapila, and S. Mudur,
    PROTERAN: Animated Terrain Evolution for Visual Analysis of Patterns in Protein Folding Trajectory,
    Bioinformatics, 23, 99-106, 2007, PMID: 17062588
  8. J. Li, Z. Yang, H. Fang, R. H. Zhou and X. Tang,
    Effect of the Carbon Nanotube Length on the Water Permeability,
    Chinese Phys. Lett., 24, 2710-2713, 2007, DOI: 10.1088/0256-307X/24/9/069
  9. A Grossfield, S E Feller, M C Pitman
    Convergence of molecular dynamics simulations of membrane proteins
    Proteins Struct. Funct. Bioinf 67, 31--40, 2007, PMID: 17243153
  10. B Fitch, A Rayshubskiy, M Eleftheriou, T Ward, M Giampapa, M Pitman, R Germain
    Progress in scaling biomolecular simulations to petaflop scale platforms
    Euro-Par 2006 workshops: parallel processing: CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics, Dresden, Germany, August 29-September 1, 2006: revised selected papers, pp. 279--288, Springer, 2007, DOI: 10.1007/978-3-540-72337-0_28
  11. F Suits, M Eleftheriou, M Giampapa, A Rayshubskiy, B Fitch, MC Pitman, TJC Ward, RS Germain
    Blue Matter on Blue Gene/L: massively parallel computation for biomolecular simulation
    Hardware/Software Codesign and System Synthesis, 2005, pp. 207--212, 2007, DOI: 10.1145/1084834.1084888

2006

  1. Kevin C Miranda, Tien Huynh, Yvonne Tay, Yen-Sin Ang, Wai-Leong Tam, Andrew M Thomson, Bing Lim, Isidore Rigoutsos
    A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
    Cell 126(6), 1203--1217, Elsevier, 2006, PMID: 16990141
  2. I Rigoutsos, T Huynh, K Miranda, A Tsirigos, A McHardy, D Platt
    Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes
    Proc. Natl. Acad. Sci. 103 (17), 6605-6610, 2006, PMID: 16636294
  3. A Grossfield, S E Feller, M C Pitman
    A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids
    Proc. Natl. Acad. Sci. 103(13), 4888, National Acad Sciences, 2006, PMID: 16547139
  4. K Mart{'i}nez-Mayorga, M C Pitman, A Grossfield, S E Feller, M F Brown
    Retinal counterion switch mechanism in vision evaluated by molecular simulations
    J. Am. Chem. Soc 128(51), 16502--16503, 2006, PMID: 17177390
  5. M. Eleftheriou, R. Germain, A. Royyuru and R. H. Zhou,
    Thermal denaturing of mutant lysozyme with both OPLSAA and CHARMM force fields,
    J. Am. Chem. Soc., 128, 13388-13395, 2006, PMID: 17031950
  6. X. Li, J. Li, M. Eleftheriou and R. H. Zhou,
    Hydration and Dewetting near Fluoronated Superhydrophobic Plates,
    J. Am. Chem. Soc., 128, 12439-12447, 2006, PMID: 16984193
  7. T. Z. Lwin, R. H. Zhou and R. Luo,
    Is Poisson-Boltzmann theory insufficient for protein folding simulations?
    J. Chem. Phys., 124, 34902-34907, 2006, PMID: 16438609
  8. P. Liu, X. Huang, R. H. Zhou and B. J., Berne,
    Hydrophobic Aided Replica Exchange Method for Protein Folding,
    J. Phys. Chem. B, 110, 19018 - 19022, 2006, PMID: 16986898
  9. A Grossfield, S E Feller, M C Pitman
    Contribution of omega-3 fatty acids to the thermodynamics of membrane protein solvation
    J. Phys. Chem. B 110(18), 8907--8909, ACS Publications, 2006, PMID: 16671691
  10. H. Lan, X. Huang, R. H. Zhou and B. J. Berne,
    Dynamics of water confined in the interdomain region of a multidomain protein,
    J. Phys. Chem. B., 110, 3704-3711, 2006, PMID: 16494427
  11. R. H. Zhou, A. Royyuru, P. Athma, F. Suits and BD Silverman,
    Magnitude and Spatial Orientation of the Hydrophobic Moments of Multi-Domain Proteins,
    Int. J. Bioinf. Res. Appl., 2, 161-176, 2006, PMID: 18048160
  12. R. H. Zhou,
    Replica Exchange Molecular Dynamics Method for Protein Folding,
    Methods Mol. Biol., 350, 205-223, 2006, PMID: 16957325
  13. T. Liu, L. Ye, H. Chen, J. Li, Z. Wu and R. H. Zhou,
    A Combined Steepest Descent and Genetic Algorithm (SD/GA) Approach for the Optimization of Solvation Parameters,
    Mol. Simul., 32, 427-435, 2006, DOI: http://dx.doi.org/10.1080/08927020600812672
  14. R. H. Zhou,
    Protein Folding with the Parallel Replica Exchange Molecular Dynamics Method,
    Parallel Computing for Bioinformatics and Computational Biology(Ed. Albert Zomaya), p397-425, John Wiley & Sons Publisher, New Jersey, 2006
  15. R. H. Zhou,
    Dewetting in Nanoscale Hydrophobic Plates Collapse and Protein Complex Folding,
    NIC Workshop 2006,From Computational Biophysics to Systems Biology, Jan Meinke, Olav Zimmermann, Sandipan Mohanty, Ulrich H.E. Hansmann (Editors), John von Neumann Institute for Computing, Jeulich,NIC Series, Vol. 34, pp. 53-58, 2006, PDF
  16. B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T.J. C. Ward, M. Giampapa, Y. Zhestkov, M. C. Pitman, F. Suits, A. Grossfield, J. Pitera, W. Swope, R. H. Zhou, S. Feller, and R. S. Germain.
    Blue Matter: Strong scaling of molecular dynamics on Blue Gene/L.
    International Conference on Computational Science (ICCS 2006), volume 3992 of LNCS, pages 846?854. Springer-Verlag, 2006.
  17. M. Eleftheriou, A. Rayshubski, J. Pitera, B. Fitch, R. H. Zhou, R. Germain,
    Large Scale Parallel Implementation of Replica Exchange on Blue Gene/L,
    SIAM Conference on Parallel Processing for Scientific Computing San Francisco, California, USA February 22-24, 2006
  18. B G Fitch, A Rayshubskiy, M Eleftheriou, TJ Ward, M Giampapa, M C Pitman, R S Germain
    Progress in scaling biomolecular simulations to petaflop scale platforms
    Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing, pp. 279--288
  19. M Eleftheriou, A Rayshubski, JW Pitera, BG Fitch, R Zhou, RS Germain
    Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L
    Parallel and Distributed Processing Symposium, 2006, pp. 8--pp
  20. B G Fitch, A Rayshubskiy, M Eleftheriou, TJ Ward, M Giampapa, M C Pitman, R S Germain
    Blue matter: Approaching the limits of concurrency for classical molecular dynamics
    Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, pp. 87--es

2005

  1. P. Liu, X. Huang, R. H. Zhou and B. J. Berne,
    Observation of a Dewetting Transition in the Collapse of the Melittin Tetramer,
    Nature, 437, 159-162, 2005, PMID: 16136146
  2. L. Ye, J. Li, T. Liu, Z. Wu and R. H. Zhou,
    Wavelets approach for protein trajectory analysis,
    J. Bioinfo. Comp. Biol., 3, 1351-1370, 2005, PMID: 16374911
  3. M C Pitman, F Suits, K Gawrisch, S E Feller
    Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers
    The Journal of chemical physics122, 244715, 2005, PMID: 16035801
  4. F Suits, M C Pitman, S E Feller
    Molecular dynamics investigation of the structural properties of phosphatidylethanolamine lipid bilayers
    The Journal of chemical physics122, 244714, 2005, PMID: 16035800
  5. J Li, T Liu, X Li, L Ye, H Chen, H Fang, Z Wu, R Zhou
    Hydration and Dewetting near Graphite- CH3 and Graphite- COOH Plates
    J. Phys. Chem. B 109(28), 13639--13648, 2005, PMID: 16852709
  6. X. Huang, R. H. Zhou, and B. J. Berne,
    Drying and Hydrophobic Collapse of Paraffin Plates,
    J. Phys. Chem. B, 109, 3546-3552, 2005, PMID: 16851392
  7. L. Parida and R. H. Zhou,
    Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a beta-hairpin,
    PLoS Comp. Biol., 1, 32-40, 2005, PMID: 16103909
  8. R. Zhou, BD Silverman, G. Dent, A. Royyuru, A. Curioni, A. Logen
    Screening and Refinement of Protein Structures from Fold Recognition
    RECOMB2005, MIT
  9. J Feng, L Parida, R Zhou
    Protein folding trajectory analysis using patterned clusters
    Asia Pacific Bioinformatics Conference, pp. 17--21, 2005
  10. O B Gene, B G Fitch, R Rayshubskiy, M Eleftheriou, T J C Ward, M Giampapa, Y Zhestkov, M C Pitman, F Suits, A Grossfield, others
    Blue Matter: Strong Scaling of Molecular Dynamics
    2005 - Citeseer, Citeseer

2004

  1. R. H. Zhou, X. Huang, C. Margulius and B. J. Berne,
    Hydrophobic Collapse in Multi-domain Protein Folding,
    Science, 305, 1605-1609, 2004, DOI: 10.1126/science.1101176
  2. R Zhou
    Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm
    Journal of Molecular Graphics and Modelling 22(5), 451--463, Elsevier, 2004, PMID: 15099840
  3. R. H. Zhou, G. Krilov and B. J. Berne,
    Comment on "Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?": The Poisson-Boltzman Model,
    J. Phys. Chem. B, 108, 7528 - 7530, 2004, DOI: 10.1021/jp037812c
  4. W. Swope, J. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B. Fitch, R. Germain, A. Rayshubskiy, T. J. C. Ward, Y. Zhestkov, and R. H. Zhou,
    Describing Protein Folding Kinetics by Molecular Dynamics Simulations: II. Application to a beta-hairpin Peptide,
    J. Phys. Chem. B, 108, 6582-6594, 2004, DOI: 10.1021/jp037422q
  5. T Huynh, I Rigoutsos
    The Web server of IBM's bioinformatics and pattern discovery group: 2004 update
    Nucleic acids research 32(suppl 2), W10, Oxford Univ Press, 2004, PMID: 15215340
  6. R. H. Zhou, A. Royyuru, P. Athma, and B. D. Silverman,
    Hydrophobicity of Multi-domain Proteins: Spatially Profiling their Distribution,
    RECOMB2004 - Currents in Computational Molecular Biology, 441-442, 2004
  7. R. H. Zhou, G. Dent, A. Royyuru, and P. Athma,
    Assessment of Protein Structure Refinement with Replica exchange Method,
    RECOMB2004 - Currents in Computational Molecular Biology, 390-391, 2004
  8. J. Feng, R. H. Zhou, and L. Parida,
    Pattern Discovery Analysis for Protein Folding Trajectories,
    Proc. 3rd Asia-Pac. Bioinfo. Conf., p95-99, Imperial College Press, London, UK, 2004
  9. I Rigoutsos, T Huynh
    Chung-kwei: a pattern-discovery-based system for the automatic identification of unsolicited e-mail messages (spam)
    Proceedings of the First Conference on Email and Anti-Spam (CEAS), 2004

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 




Members


Alumni

  • Otitoaleke G. Akinola
  • David R. Bell
  • Matteo Castelli
  • Camilo Jimenez
  • Yuxing Peng
  • Michael Pitman
  • Raul Araya Secchi
  • Frank Suits
  • Jacinta Wubben
  • Zhen Xia
  • Payel Das